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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.7.dev0

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        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2020-03-08, 10:14 based on data in: /ssd/gaulkec_temp_ht_meta/data/raw_multiqc/input


        General Statistics

        Showing 200/200 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        lane7-s014-indexRPI2-CGATGT-YZ5-1-NEXTFLEXRapidXP_S14_L007_R1_001
        10.7%
        46%
        3.6
        lane7-s015-indexRPI4-TGACCA-YZ5-2-NEXTFLEXRapidXP_S15_L007_R1_001
        9.9%
        46%
        4.1
        lane7-s016-indexRPI5-ACAGTG-YZ5-3-NEXTFLEXRapidXP_S16_L007_R1_001
        9.0%
        46%
        2.8
        lane7-s017-indexRPI6-GCCAAT-YZ5-4-NEXTFLEXRapidXP_S17_L007_R1_001
        10.6%
        46%
        2.7
        lane7-s018-indexRPI7-CAGATC-YZ5-5-NEXTFLEXRapidXP_S18_L007_R1_001
        8.7%
        46%
        2.7
        lane7-s019-indexRPI12-CTTGTA-ACR-134-1-NEXTFLEXRapidXP_S19_L007_R1_001
        14.3%
        39%
        2.1
        lane7-s020-indexRPI1-ATCACG-ACR-134-2-NEXTFLEXRapidXP_S20_L007_R1_001
        11.9%
        38%
        1.7
        lane7-s021-index-TTAGGC-ACR-134-3-NEXTFLEXRapidXP_S21_L007_R1_001
        13.1%
        39%
        1.9
        lane7-s022-indexRPI8-ACTTGA-ACR-134-4-NEXTFLEXRapidXP_S22_L007_R1_001
        14.6%
        39%
        1.5
        lane7-s023-indexRPI9-GATCAG-ACR-134-5-NEXTFLEXRapidXP_S23_L007_R1_001
        12.8%
        39%
        2.1
        lane7-s024-indexRPI10-TAGCTT-SHI-Plate1-A1-1-NEXTFLEXRapidXP_S24_L007_R1_001
        8.2%
        61%
        5.0
        lane7-s025-indexRPI11-GGCTAC-SHI-Plate1-A1-2-NEXTFLEXRapidXP_S25_L007_R1_001
        7.2%
        61%
        4.0
        lane7-s026-indexRPI25-ACTGAT-SHI-Plate1-A1-3-NEXTFLEXRapidXP_S26_L007_R1_001
        8.3%
        61%
        4.5
        lane7-s027-indexRPI26-ATGAGC-SHI-Plate1-A1-4-NEXTFLEXRapidXP_S27_L007_R1_001
        6.9%
        61%
        3.2
        lane7-s028-indexRPI27-ATTCCT-SHI-Plate1-A1-5-NEXTFLEXRapidXP_S28_L007_R1_001
        7.2%
        61%
        3.9
        lane7-s029-indexRPI28-CAAAAG-Mock-1-NEXTFLEXRapidXP_S29_L007_R1_001
        11.0%
        48%
        3.7
        lane7-s030-indexRPI29-CAACTA-Mock-2-NEXTFLEXRapidXP_S30_L007_R1_001
        11.8%
        48%
        4.2
        lane7-s031-indexRPI30-CACCGG-Mock-3-NEXTFLEXRapidXP_S31_L007_R1_001
        11.1%
        48%
        4.0
        lane7-s032-indexRPI31-CACGAT-Mock-4-NEXTFLEXRapidXP_S32_L007_R1_001
        13.1%
        48%
        5.0
        lane7-s033-indexRPI32-CACTCA-Mock-5-NEXTFLEXRapidXP_S33_L007_R1_001
        12.4%
        47%
        5.0
        lane7-s097-index-TTGGAATG-YZ5-1-plexWell96-1_S97_L007_R1_001
        10.6%
        46%
        0.5
        lane7-s098-index-GGGACAAC-YZ5-2-plexWell96-2_S98_L007_R1_001
        10.4%
        46%
        0.7
        lane7-s099-index-GCTGGATC-YZ5-3-plexWell96-3_S99_L007_R1_001
        11.2%
        46%
        0.8
        lane7-s100-index-ACACTCAA-YZ5-4-plexWell96-4_S100_L007_R1_001
        10.3%
        46%
        0.4
        lane7-s101-index-ACTAGCTA-YZ5-5-plexWell96-5_S101_L007_R1_001
        11.9%
        46%
        0.7
        lane7-s102-index-GATGATTG-ACR-134-1-plexWell96-6_S102_L007_R1_001
        12.2%
        39%
        0.9
        lane7-s103-index-GCAATCTT-ACR-134-2-plexWell96-7_S103_L007_R1_001
        13.5%
        39%
        0.9
        lane7-s104-index-AGAGTGTC-ACR-134-3-plexWell96-8_S104_L007_R1_001
        11.8%
        40%
        0.2
        lane7-s105-index-TTAATGCG-ACR-134-4-plexWell96-9_S105_L007_R1_001
        12.0%
        40%
        0.6
        lane7-s106-index-TCCTATAT-ACR-134-5-plexWell96-10_S106_L007_R1_001
        15.7%
        39%
        1.2
        lane7-s107-index-CCATATCC-SHI-Plate1-A1-1-plexWell96-11_S107_L007_R1_001
        9.9%
        59%
        1.3
        lane7-s108-index-AGCCGACG-SHI-Plate1-A1-2-plexWell96-12_S108_L007_R1_001
        9.7%
        60%
        0.4
        lane7-s109-index-CGAATTCA-SHI-Plate1-A1-3-plexWell96-13_S109_L007_R1_001
        9.3%
        59%
        0.8
        lane7-s110-index-GTCAGACC-SHI-Plate1-A1-4-plexWell96-14_S110_L007_R1_001
        9.9%
        60%
        1.1
        lane7-s111-index-CATTGCCT-SHI-Plate1-A1-5-plexWell96-15_S111_L007_R1_001
        11.4%
        59%
        0.8
        lane7-s112-index-TAACCGCA-Mock-1-plexWell96-16_S112_L007_R1_001
        13.6%
        47%
        0.9
        lane7-s113-index-GCGCGAAG-Mock-2-plexWell96-17_S113_L007_R1_001
        10.8%
        47%
        0.4
        lane7-s114-index-AACACGTG-Mock-3-plexWell96-18_S114_L007_R1_001
        13.4%
        47%
        1.3
        lane7-s115-index-GTAGTCAC-Mock-4-plexWell96-19_S115_L007_R1_001
        12.1%
        47%
        0.9
        lane7-s116-index-GAGTTCTC-Mock-5-plexWell96-20_S116_L007_R1_001
        17.9%
        48%
        2.4
        lane7-s117-index-GTGAGGAA-YZ5-1-plexWell96-21_S117_L007_R1_001
        11.1%
        46%
        0.6
        lane7-s118-index-GATTCGTA-YZ5-2-plexWell96-22_S118_L007_R1_001
        11.0%
        46%
        0.7
        lane7-s119-index-GATGCAAT-YZ5-3-plexWell96-23_S119_L007_R1_001
        12.0%
        46%
        0.8
        lane7-s120-index-ACACGGTT-YZ5-4-plexWell96-24_S120_L007_R1_001
        12.0%
        46%
        0.7
        lane7-s121-index-GAGGCTGC-YZ5-5-plexWell96-25_S121_L007_R1_001
        11.7%
        46%
        1.2
        lane7-s122-index-ACAGTTCG-ACR-134-1-plexWell96-26_S122_L007_R1_001
        12.4%
        39%
        0.8
        lane7-s123-index-CGGAGATA-ACR-134-2-plexWell96-27_S123_L007_R1_001
        13.1%
        40%
        0.8
        lane7-s124-index-TCGCCAGC-ACR-134-3-plexWell96-28_S124_L007_R1_001
        13.4%
        40%
        1.1
        lane7-s125-index-TGCACTGT-ACR-134-4-plexWell96-29_S125_L007_R1_001
        13.3%
        40%
        0.5
        lane7-s126-index-GTACGCGA-ACR-134-5-plexWell96-30_S126_L007_R1_001
        14.7%
        39%
        1.7
        lane7-s127-index-CTATCCGG-SHI-Plate1-A1-1-plexWell96-31_S127_L007_R1_001
        9.4%
        60%
        1.7
        lane7-s128-index-CTTAGAGT-SHI-Plate1-A1-2-plexWell96-32_S128_L007_R1_001
        10.9%
        60%
        1.5
        lane7-s129-index-CAAGGACC-SHI-Plate1-A1-3-plexWell96-33_S129_L007_R1_001
        10.4%
        60%
        1.8
        lane7-s130-index-AGACAGAG-SHI-Plate1-A1-4-plexWell96-34_S130_L007_R1_001
        11.5%
        59%
        0.1
        lane7-s131-index-TCGGATCA-SHI-Plate1-A1-5-plexWell96-35_S131_L007_R1_001
        10.6%
        59%
        0.4
        lane7-s132-index-TAATGGAC-Mock-1-plexWell96-36_S132_L007_R1_001
        12.8%
        47%
        0.8
        lane7-s133-index-TAGCAACT-Mock-2-plexWell96-37_S133_L007_R1_001
        13.4%
        47%
        0.9
        lane7-s134-index-ATAGCACA-Mock-3-plexWell96-38_S134_L007_R1_001
        12.7%
        47%
        0.6
        lane7-s135-index-ATCAACCG-Mock-4-plexWell96-39_S135_L007_R1_001
        10.3%
        47%
        0.5
        lane7-s136-index-TTCCTCAT-Mock-5-plexWell96-40_S136_L007_R1_001
        19.0%
        47%
        2.1
        lane7-s137-index-AGCTACGT-YZ5-1-plexWell96-41_S137_L007_R1_001
        11.4%
        46%
        0.4
        lane7-s138-index-ATTCCATC-YZ5-2-plexWell96-42_S138_L007_R1_001
        10.5%
        46%
        0.6
        lane7-s139-index-GTTGTAGG-YZ5-3-plexWell96-43_S139_L007_R1_001
        10.3%
        46%
        0.6
        lane7-s140-index-TGTGACTA-YZ5-4-plexWell96-44_S140_L007_R1_001
        11.3%
        46%
        0.6
        lane7-s141-index-CGAAACGC-YZ5-5-plexWell96-45_S141_L007_R1_001
        11.5%
        46%
        0.9
        lane7-s142-index-GTGTGATT-ACR-134-1-plexWell96-46_S142_L007_R1_001
        14.3%
        39%
        1.1
        lane7-s143-index-AGGCTGGA-ACR-134-2-plexWell96-47_S143_L007_R1_001
        11.6%
        40%
        0.2
        lane7-s144-index-CGTGCTGG-ACR-134-3-plexWell96-48_S144_L007_R1_001
        13.1%
        40%
        1.2
        lane7-s145-index-AATAGGAT-ACR-134-4-plexWell96-49_S145_L007_R1_001
        13.5%
        40%
        0.7
        lane7-s146-index-CGTCTGCC-ACR-134-5-plexWell96-50_S146_L007_R1_001
        14.1%
        40%
        1.2
        lane7-s147-index-GAATCTAG-SHI-Plate1-A1-1-plexWell96-51_S147_L007_R1_001
        8.8%
        60%
        1.1
        lane7-s148-index-ATGCGTCA-SHI-Plate1-A1-2-plexWell96-52_S148_L007_R1_001
        10.4%
        59%
        1.0
        lane7-s149-index-GCAAGTAC-SHI-Plate1-A1-3-plexWell96-53_S149_L007_R1_001
        10.3%
        60%
        1.4
        lane7-s150-index-ACTGACCT-SHI-Plate1-A1-4-plexWell96-54_S150_L007_R1_001
        11.2%
        60%
        0.8
        lane7-s151-index-GAAGACCA-SHI-Plate1-A1-5-plexWell96-55_S151_L007_R1_001
        9.7%
        59%
        1.5
        lane7-s152-index-CAGAAGCG-Mock-1-plexWell96-56_S152_L007_R1_001
        13.5%
        47%
        1.1
        lane7-s153-index-AGCTCTAC-Mock-2-plexWell96-57_S153_L007_R1_001
        17.5%
        47%
        0.2
        lane7-s154-index-CCACTACT-Mock-3-plexWell96-58_S154_L007_R1_001
        13.9%
        47%
        1.0
        lane7-s155-index-GACCTACA-Mock-4-plexWell96-59_S155_L007_R1_001
        8.3%
        47%
        0.5
        lane7-s156-index-CACGTCCG-Mock-5-plexWell96-60_S156_L007_R1_001
        16.2%
        47%
        2.0
        lane7-s551-index--TAAGGCGA-CTCCTTAC-YZ5-1-NexteraFlex-Full_S551_L007_R1_001
        21.7%
        45%
        5.7
        lane7-s552-index--CGTACTAG-TCTTACGC-YZ5-2-NexteraFlex-Full_S552_L007_R1_001
        15.5%
        45%
        3.2
        lane7-s553-index--AGGCAGAA-TATGCAGT-YZ5-3-NexteraFlex-Full_S553_L007_R1_001
        16.2%
        45%
        2.9
        lane7-s554-index--GGACTCCT-AGAGGATA-YZ5-4-NexteraFlex-Full_S554_L007_R1_001
        17.0%
        45%
        3.0
        lane7-s555-index--TAGGCATG-ACTCTAGG-YZ5-5-NexteraFlex-Full_S555_L007_R1_001
        13.0%
        45%
        2.3
        lane7-s556-index--CGAGGCTG-TCGCATAA-ACR-134-1-NexteraFlex-Full_S556_L007_R1_001
        12.6%
        39%
        1.9
        lane7-s557-index--AAGAGGCA-CTAGTCGA-ACR-134-2-NexteraFlex-Full_S557_L007_R1_001
        15.3%
        39%
        3.2
        lane7-s558-index--GCTCATGA-ATTAGACG-ACR-134-3-NexteraFlex-Full_S558_L007_R1_001
        14.2%
        39%
        3.1
        lane7-s559-index--CGTACTAG-TATGCAGT-ACR-134-4-NexteraFlex-Full_S559_L007_R1_001
        14.9%
        39%
        3.4
        lane7-s560-index--AGGCAGAA-CTCCTTAC-ACR-134-5-NexteraFlex-Full_S560_L007_R1_001
        14.7%
        39%
        5.3
        lane7-s561-index--TAAGGCGA-TCTTACGC-SHI-Plate1-A1-1-NexteraFlex-Full_S561_L007_R1_001
        7.2%
        59%
        3.4
        lane7-s562-index--CTCTCTAC-AGAGGATA-SHI-Plate1-A1-2-NexteraFlex-Full_S562_L007_R1_001
        7.4%
        59%
        3.1
        lane7-s563-index--GTAGAGGA-ACTCTAGG-SHI-Plate1-A1-3-NexteraFlex-Full_S563_L007_R1_001
        7.1%
        59%
        2.7
        lane7-s564-index--AAGAGGCA-ATTAGACG-SHI-Plate1-A1-4-NexteraFlex-Full_S564_L007_R1_001
        8.0%
        59%
        4.5
        lane7-s565-index--GCTCATGA-TCGCATAA-SHI-Plate1-A1-5-NexteraFlex-Full_S565_L007_R1_001
        5.8%
        59%
        2.6
        lane7-s566-index--CGAGGCTG-CTAGTCGA-Mock-1-NexteraFlex-Full_S566_L007_R1_001
        21.9%
        46%
        3.8
        lane7-s567-index--AGGCAGAA-TCTTACGC-Mock-2-NexteraFlex-Full_S567_L007_R1_001
        21.8%
        46%
        3.7
        lane7-s568-index--TAAGGCGA-TATGCAGT-Mock-3-NexteraFlex-Full_S568_L007_R1_001
        27.0%
        45%
        5.4
        lane7-s569-index--CGTACTAG-CTCCTTAC-Mock-4-NexteraFlex-Full_S569_L007_R1_001
        18.5%
        46%
        2.5
        lane7-s570-index--TAGCGCTC-AGAGGATA-Mock-5-NexteraFlex-Full_S570_L007_R1_001
        29.4%
        46%
        7.9
        lane7-s571-index--GGACTCCT-CTCCTTAC-YZ5-1-NexteraFlex-Reduced_S571_L007_R1_001
        10.3%
        44%
        3.1
        lane7-s572-index--CTCTCTAC-TCTTACGC-YZ5-2-NexteraFlex-Reduced_S572_L007_R1_001
        10.2%
        44%
        3.5
        lane7-s573-index--TAGCGCTC-TATGCAGT-YZ5-3-NexteraFlex-Reduced_S573_L007_R1_001
        9.5%
        44%
        2.6
        lane7-s574-index--TAGGCATG-AGAGGATA-YZ5-4-NexteraFlex-Reduced_S574_L007_R1_001
        9.7%
        44%
        3.0
        lane7-s575-index--CGAGGCTG-ACTCTAGG-YZ5-5-NexteraFlex-Reduced_S575_L007_R1_001
        11.6%
        44%
        5.5
        lane7-s576-index--TAAGGCGA-TCGCATAA-ACR-134-1-NexteraFlex-Reduced_S576_L007_R1_001
        12.3%
        39%
        2.8
        lane7-s577-index--CGTACTAG-CTAGTCGA-ACR-134-2-NexteraFlex-Reduced_S577_L007_R1_001
        12.1%
        39%
        3.0
        lane7-s578-index--AGGCAGAA-ATTAGACG-ACR-134-3-NexteraFlex-Reduced_S578_L007_R1_001
        12.5%
        40%
        3.8
        lane7-s579-index--CTCTCTAC-TATGCAGT-ACR-134-4-NexteraFlex-Reduced_S579_L007_R1_001
        13.6%
        40%
        4.3
        lane7-s580-index--TAGCGCTC-CTCCTTAC-ACR-134-5-NexteraFlex-Reduced_S580_L007_R1_001
        13.8%
        39%
        4.6
        lane7-s581-index--GGACTCCT-TCTTACGC-SHI-Plate1-A1-1-NexteraFlex-Reduced_S581_L007_R1_001
        8.1%
        57%
        4.4
        lane7-s582-index--GTAGAGGA-AGAGGATA-SHI-Plate1-A1-2-NexteraFlex-Reduced_S582_L007_R1_001
        7.5%
        56%
        5.4
        lane7-s583-index--AAGAGGCA-ACTCTAGG-SHI-Plate1-A1-3-NexteraFlex-Reduced_S583_L007_R1_001
        7.3%
        56%
        4.2
        lane7-s584-index--CGTACTAG-ATTAGACG-SHI-Plate1-A1-4-NexteraFlex-Reduced_S584_L007_R1_001
        7.0%
        56%
        2.5
        lane7-s585-index--AGGCAGAA-TCGCATAA-SHI-Plate1-A1-5-NexteraFlex-Reduced_S585_L007_R1_001
        6.6%
        57%
        5.0
        lane7-s586-index--TAAGGCGA-CTAGTCGA-Mock-1-NexteraFlex-Reduced_S586_L007_R1_001
        21.6%
        43%
        4.7
        lane7-s587-index--CGGAGCCT-ACTCTAGG-Mock-2-NexteraFlex-Reduced_S587_L007_R1_001
        22.9%
        44%
        5.2
        lane7-s588-index--GCTCATGA-CTAGTCGA-Mock-3-NexteraFlex-Reduced_S588_L007_R1_001
        18.5%
        43%
        3.7
        lane7-s589-index--CGAGGCTG-ATTAGACG-Mock-4-NexteraFlex-Reduced_S589_L007_R1_001
        17.7%
        44%
        3.4
        lane7-s590-index--AAGAGGCA-TCGCATAA-Mock-5-NexteraFlex-Reduced_S590_L007_R1_001
        21.8%
        43%
        4.9
        lane7-s591-index--ATTACTCG-AGGCTATA-YZ5-1-QIAseqFX_S591_L007_R1_001
        11.0%
        46%
        3.2
        lane7-s592-index--ATTACTCG-GCCTCTAT-YZ5-2-QIAseqFX_S592_L007_R1_001
        9.9%
        46%
        3.3
        lane7-s593-index--ATTACTCG-AGGATAGG-YZ5-3-QIAseqFX_S593_L007_R1_001
        10.1%
        46%
        2.9
        lane7-s594-index--ATTACTCG-TCAGAGCC-YZ5-4-QIAseqFX_S594_L007_R1_001
        11.7%
        45%
        3.0
        lane7-s595-index--ATTACTCG-CTTCGCCT-YZ5-5-QIAseqFX_S595_L007_R1_001
        8.5%
        46%
        2.1
        lane7-s596-index--ATTACTCG-TAAGATTA-ACR-134-1-QIAseqFX_S596_L007_R1_001
        15.4%
        39%
        2.7
        lane7-s597-index--ATTACTCG-ACGTCCTG-ACR-134-2-QIAseqFX_S597_L007_R1_001
        13.7%
        39%
        2.4
        lane7-s598-index--ATTACTCG-GTCAGTAC-ACR-134-3-QIAseqFX_S598_L007_R1_001
        22.4%
        38%
        1.1
        lane7-s599-index--TCCGGAGA-AGGCTATA-ACR-134-4-QIAseqFX_S599_L007_R1_001
        21.5%
        39%
        2.4
        lane7-s600-index--TCCGGAGA-GCCTCTAT-ACR-134-5-QIAseqFX_S600_L007_R1_001
        14.8%
        39%
        3.6
        lane7-s601-index--TCCGGAGA-AGGATAGG-SHI-Plate1-A1-1-QIAseqFX_S601_L007_R1_001
        8.5%
        60%
        3.3
        lane7-s602-index--TCCGGAGA-TCAGAGCC-SHI-Plate1-A1-2-QIAseqFX_S602_L007_R1_001
        9.2%
        60%
        5.7
        lane7-s603-index--TCCGGAGA-CTTCGCCT-SHI-Plate1-A1-3-QIAseqFX_S603_L007_R1_001
        8.2%
        60%
        4.1
        lane7-s604-index--TCCGGAGA-TAAGATTA-SHI-Plate1-A1-4-QIAseqFX_S604_L007_R1_001
        8.3%
        60%
        1.5
        lane7-s605-index--TCCGGAGA-ACGTCCTG-SHI-Plate1-A1-5-QIAseqFX_S605_L007_R1_001
        6.4%
        60%
        3.7
        lane7-s606-index--TCCGGAGA-GTCAGTAC-Mock-1-QIAseqFX_S606_L007_R1_001
        14.8%
        47%
        3.5
        lane7-s607-index--CGCTCATT-AGGCTATA-Mock-2-QIAseqFX_S607_L007_R1_001
        13.6%
        47%
        3.4
        lane7-s608-index--CGCTCATT-GCCTCTAT-Mock-3-rd2-QIAseqFX_S608_L007_R1_001
        13.4%
        47%
        2.8
        lane7-s609-index--CGCTCATT-AGGATAGG-Mock-4-rd2-QIAseqFX_S609_L007_R1_001
        12.5%
        47%
        3.0
        lane7-s610-index--CGCTCATT-TCAGAGCC-Mock-5-QIAseqFX_S610_L007_R1_001
        11.8%
        46%
        2.9
        lane7-s611-index--TTGGAATG-ATAGAGAG-YZ5-1-plexWell96-1_S611_L007_R1_001
        9.9%
        46%
        0.4
        lane7-s612-index--GGGACAAC-ATAGAGAG-YZ5-2-plexWell96-2_S612_L007_R1_001
        9.6%
        46%
        0.6
        lane7-s613-index--GCTGGATC-ATAGAGAG-YZ5-3-plexWell96-3_S613_L007_R1_001
        10.4%
        46%
        0.7
        lane7-s614-index--ACACTCAA-ATAGAGAG-YZ5-4-plexWell96-4_S614_L007_R1_001
        10.0%
        46%
        0.3
        lane7-s615-index--ACTAGCTA-ATAGAGAG-YZ5-5-plexWell96-5_S615_L007_R1_001
        11.6%
        46%
        0.6
        lane7-s616-index--GATGATTG-ATAGAGAG-ACR-134-1-plexWell96-6_S616_L007_R1_001
        11.8%
        39%
        0.8
        lane7-s617-index--GCAATCTT-ATAGAGAG-ACR-134-2-plexWell96-7_S617_L007_R1_001
        13.4%
        39%
        0.8
        lane7-s618-index--AGAGTGTC-ATAGAGAG-ACR-134-3-plexWell96-8_S618_L007_R1_001
        11.6%
        40%
        0.2
        lane7-s619-index--TTAATGCG-ATAGAGAG-ACR-134-4-plexWell96-9_S619_L007_R1_001
        11.8%
        39%
        0.5
        lane7-s620-index--TCCTATAT-ATAGAGAG-ACR-134-5-plexWell96-10_S620_L007_R1_001
        15.6%
        39%
        1.1
        lane7-s621-index--CCATATCC-ATAGAGAG-SHI-Plate1-A1-1-plexWell96-11_S621_L007_R1_001
        9.2%
        59%
        1.1
        lane7-s622-index--AGCCGACG-ATAGAGAG-SHI-Plate1-A1-2-plexWell96-12_S622_L007_R1_001
        9.4%
        60%
        0.4
        lane7-s623-index--CGAATTCA-ATAGAGAG-SHI-Plate1-A1-3-plexWell96-13_S623_L007_R1_001
        9.1%
        59%
        0.7
        lane7-s624-index--GTCAGACC-ATAGAGAG-SHI-Plate1-A1-4-plexWell96-14_S624_L007_R1_001
        9.3%
        60%
        0.9
        lane7-s625-index--CATTGCCT-ATAGAGAG-SHI-Plate1-A1-5-plexWell96-15_S625_L007_R1_001
        11.2%
        59%
        0.7
        lane7-s626-index--TAACCGCA-ATAGAGAG-Mock-1-plexWell96-16_S626_L007_R1_001
        12.9%
        47%
        0.8
        lane7-s627-index--GCGCGAAG-ATAGAGAG-Mock-2-plexWell96-17_S627_L007_R1_001
        10.0%
        47%
        0.4
        lane7-s628-index--AACACGTG-ATAGAGAG-Mock-3-plexWell96-18_S628_L007_R1_001
        11.5%
        47%
        1.0
        lane7-s629-index--GTAGTCAC-ATAGAGAG-Mock-4-plexWell96-19_S629_L007_R1_001
        11.2%
        47%
        0.8
        lane7-s630-index--GAGTTCTC-ATAGAGAG-Mock-5-plexWell96-20_S630_L007_R1_001
        16.4%
        47%
        2.0
        lane7-s631-index--GTGAGGAA-ATAGAGAG-YZ5-1-plexWell96-21_S631_L007_R1_001
        10.6%
        46%
        0.5
        lane7-s632-index--GATTCGTA-ATAGAGAG-YZ5-2-plexWell96-22_S632_L007_R1_001
        10.7%
        46%
        0.6
        lane7-s633-index--GATGCAAT-ATAGAGAG-YZ5-3-plexWell96-23_S633_L007_R1_001
        11.8%
        46%
        0.7
        lane7-s634-index--ACACGGTT-ATAGAGAG-YZ5-4-plexWell96-24_S634_L007_R1_001
        11.7%
        46%
        0.7
        lane7-s635-index--GAGGCTGC-ATAGAGAG-YZ5-5-plexWell96-25_S635_L007_R1_001
        10.7%
        46%
        1.0
        lane7-s636-index--ACAGTTCG-ATAGAGAG-ACR-134-1-plexWell96-26_S636_L007_R1_001
        12.2%
        39%
        0.7
        lane7-s637-index--CGGAGATA-ATAGAGAG-ACR-134-2-plexWell96-27_S637_L007_R1_001
        12.8%
        40%
        0.7
        lane7-s638-index--TCGCCAGC-ATAGAGAG-ACR-134-3-plexWell96-28_S638_L007_R1_001
        12.6%
        40%
        0.9
        lane7-s639-index--TGCACTGT-ATAGAGAG-ACR-134-4-plexWell96-29_S639_L007_R1_001
        13.1%
        40%
        0.5
        lane7-s640-index--GTACGCGA-ATAGAGAG-ACR-134-5-plexWell96-30_S640_L007_R1_001
        14.4%
        39%
        1.5
        lane7-s641-index--CTATCCGG-ATAGAGAG-SHI-Plate1-A1-1-plexWell96-31_S641_L007_R1_001
        8.5%
        60%
        1.4
        lane7-s642-index--CTTAGAGT-ATAGAGAG-SHI-Plate1-A1-2-plexWell96-32_S642_L007_R1_001
        10.7%
        60%
        1.3
        lane7-s643-index--CAAGGACC-ATAGAGAG-SHI-Plate1-A1-3-plexWell96-33_S643_L007_R1_001
        9.6%
        59%
        1.4
        lane7-s644-index--AGACAGAG-ATAGAGAG-SHI-Plate1-A1-4-plexWell96-34_S644_L007_R1_001
        10.7%
        59%
        0.1
        lane7-s645-index--TCGGATCA-ATAGAGAG-SHI-Plate1-A1-5-plexWell96-35_S645_L007_R1_001
        10.1%
        59%
        0.4
        lane7-s646-index--TAATGGAC-ATAGAGAG-Mock-1-plexWell96-36_S646_L007_R1_001
        12.0%
        47%
        0.7
        lane7-s647-index--TAGCAACT-ATAGAGAG-Mock-2-plexWell96-37_S647_L007_R1_001
        13.0%
        47%
        0.8
        lane7-s648-index--ATAGCACA-ATAGAGAG-Mock-3-plexWell96-38_S648_L007_R1_001
        12.2%
        47%
        0.6
        lane7-s649-index--ATCAACCG-ATAGAGAG-Mock-4-plexWell96-39_S649_L007_R1_001
        10.1%
        47%
        0.5
        lane7-s650-index--TTCCTCAT-ATAGAGAG-Mock-5-plexWell96-40_S650_L007_R1_001
        18.4%
        47%
        1.9
        lane7-s651-index--AGCTACGT-ATAGAGAG-YZ5-1-plexWell96-41_S651_L007_R1_001
        11.3%
        46%
        0.4
        lane7-s652-index--ATTCCATC-ATAGAGAG-YZ5-2-plexWell96-42_S652_L007_R1_001
        10.2%
        46%
        0.5
        lane7-s653-index--GTTGTAGG-ATAGAGAG-YZ5-3-plexWell96-43_S653_L007_R1_001
        9.5%
        46%
        0.5
        lane7-s654-index--TGTGACTA-ATAGAGAG-YZ5-4-plexWell96-44_S654_L007_R1_001
        11.0%
        46%
        0.5
        lane7-s655-index--CGAAACGC-ATAGAGAG-YZ5-5-plexWell96-45_S655_L007_R1_001
        10.7%
        46%
        0.7
        lane7-s656-index--GTGTGATT-ATAGAGAG-ACR-134-1-plexWell96-46_S656_L007_R1_001
        14.2%
        39%
        1.0
        lane7-s657-index--AGGCTGGA-ATAGAGAG-ACR-134-2-plexWell96-47_S657_L007_R1_001
        17.1%
        40%
        0.2
        lane7-s658-index--CGTGCTGG-ATAGAGAG-ACR-134-3-plexWell96-48_S658_L007_R1_001
        12.4%
        40%
        1.1
        lane7-s659-index--AATAGGAT-ATAGAGAG-ACR-134-4-plexWell96-49_S659_L007_R1_001
        13.4%
        40%
        0.6
        lane7-s660-index--CGTCTGCC-ATAGAGAG-ACR-134-5-plexWell96-50_S660_L007_R1_001
        13.7%
        39%
        1.1
        lane7-s661-index--GAATCTAG-ATAGAGAG-SHI-Plate1-A1-1-plexWell96-51_S661_L007_R1_001
        8.3%
        60%
        1.0
        lane7-s662-index--ATGCGTCA-ATAGAGAG-SHI-Plate1-A1-2-plexWell96-52_S662_L007_R1_001
        10.0%
        59%
        0.9
        lane7-s663-index--GCAAGTAC-ATAGAGAG-SHI-Plate1-A1-3-plexWell96-53_S663_L007_R1_001
        9.7%
        60%
        1.2
        lane7-s664-index--ACTGACCT-ATAGAGAG-SHI-Plate1-A1-4-plexWell96-54_S664_L007_R1_001
        11.0%
        60%
        0.7
        lane7-s665-index--GAAGACCA-ATAGAGAG-SHI-Plate1-A1-5-plexWell96-55_S665_L007_R1_001
        9.3%
        59%
        1.3
        lane7-s666-index--CAGAAGCG-ATAGAGAG-Mock-1-plexWell96-56_S666_L007_R1_001
        12.6%
        47%
        1.0
        lane7-s667-index--AGCTCTAC-ATAGAGAG-Mock-2-plexWell96-57_S667_L007_R1_001
        15.8%
        47%
        0.2
        lane7-s668-index--CCACTACT-ATAGAGAG-Mock-3-plexWell96-58_S668_L007_R1_001
        13.4%
        47%
        0.9
        lane7-s669-index--GACCTACA-ATAGAGAG-Mock-4-plexWell96-59_S669_L007_R1_001
        8.3%
        47%
        0.4
        lane7-s670-index--CACGTCCG-ATAGAGAG-Mock-5-plexWell96-60_S670_L007_R1_001
        15.4%
        47%
        1.8

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (151bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).